From The Shadows
by Evil Jeremy
Summary: In 1994, Franz Hopper stole government research. Now, 12 years later, they want it back. As the government closes in on the Lyoko warriors, Aelita will stop at nothing to protect her father's research, regardless of the consequences.
1. Introduction

**Introduction to "From The Shadows"**

**Hello folks. I'm EvilJeremy, EJ for short as I will go by now. I've been writing fanfiction for Code Lyoko (aka my childhood) since around 2006 I believe, although I haven't written in around 2 years (my last story, Project ZAIA, remains unfinished unfortunately). The return of Code Lyoko has inspired me to return to writing. Like all my other stories, this one will be heavily serialized, with an overarching story built into the mythology of the show. Also, I refer to my stories as "seasons" and my chapters as "episodes". Oh, and before I forget, the necessary disclaimer:**

**I own Code Lyoko, and all the characters and locations. That includes France. I also own McDonalds, the Steelers, and the moon.**

**Ok, I might have been exaggerating a bit.**

**Anyways, enjoy the read, and please review/follow/favorite (those last two features didn't even exist here 2 years ago. Wow times have changed)!**


	2. Episode 1: 6 Months Later

**Episode 1: 6 Months Later**

**PS: I don't actually own these characters!**

* * *

"The white rain fell, from the shadows of hell,  
And all I knew was gone.  
Peace at a price, my sacrifice,  
The decision I made at dawn.  
Preventing a war, like none from before,  
While the darkness starts to descend.  
And every night I pray, I'll see you again one day,  
In the valley where all roads end."

* * *

December, 2005

Aelita's eyes shot wide open, as her heart pounded rapidly. Another night, another nightmare. It had been a while since Aelita had a solid night's sleep. Disoriented, Aelita got out of bed and wobbled over to her desk, where a full glass of water was sitting. Her hands shaking, she picked up the glass and started gulping the water as quickly as possible, as cold sweat ran down her forehead.

"It's unlocked" Jeremy said from his desk, after hearing knocking on his door. Aelita entered the room, still shaking from her nightmare. Jeremy looked around, noticed her condition, and immediately jumped out of his chair and over to Aelita. "It's ok" he said as he embraced Aelita. "You're going to be ok" he repeated as he guided her down to his bed.

"Same dream?" he asked calmly. "It hardly qualifies as a dream" Aelita shot back. "More of a reminder."

"XANA can't hurt us anymore. He hasn't been able to hurt anyone for, what has it been, half a year now?" Jeremy reassured Aelita. "Then why can't I rest?" Aelita wondered.

It was starting to snow outside, as it tends to do in the winter months. Christmas was quickly approaching, along with the end of the fall semester. Aelita, Odd, Jeremy, and Ulrich were in 10th grade, with Yumi in 11th. Important years in one's adolescence and not some that should include sleep disorders. Aelita gazed out Jeremy's window, observing the falling snow.

"It was snowing the last time I saw my mother" Aelita noted quietly. "I wish I knew what happened to her".

Jeremy wrapped his arms around Aelita and pulled her close. She laid her head on his shoulder, and he rested his head over hers. The two sat quietly, on his bed in the corner of the room, looking out at the snow building up.

* * *

"Odd, turn off your damn alarm" Ulrich yelled, using his pillow to cover his ears from the techno music filling their dorm room. "It's the Subdigitals latest track, isn't it awesome?" Odd said from the bathroom, his voice muffled by the toothbrush (and paste) in his mouth. "Their album doesn't even come out until March, how did you get this song?" "Jeremy used his computer magic to get it for me".

Odd walked back over to his phone and turned off the music. "What's up buddy, you love the Subdigitals" Odd commented. "I'm not really in the mood for music right now" Ulrich groaned, pulling his bed sheets over his head. "What time is it?" he asked Odd through his sheets. "7:48" Odd said as he put on his jacket. "Seriously?" Ulrich questioned as he jumped out of bed.

"I have breakfast with Yumi at 8"

"Kiwi thinks you need to set up your own alarm"

"Well you tell Kiwi that I'd wake up in the morning if his barks didn't keep me up all night" Ulrich grunted as he exited the room.

"Hey, my dog has feelings too!" Odd shouted after him.

* * *

"Still having issues staying asleep?" Yolanda the nurse asked Aelita. "Unfortunately" Aelita responded, her voice hushed as she stared at the ground. "Well, as much as I'd love to help, I can't prescribe you any sedatives, and I can't defer you to a psychiatrist since you still haven't given me your health records" Yolanda said, swiveling around the room on her chair. "Damn," Aelita thought to herself. "Keep forgetting to remind Jeremy to doctor those records".

Yolanda walked up to her medicine cabinet, and searched for a few moments before pulling out a small bottle. "This is Melatonin, it's a sleeping aid. Take one pill every night, it should help you stay asleep at night".

* * *

"You look spiffy" Yumi nodded towards Ulrich.

"Don't blame me" Ulrich said as he sat down across from Yumi in the cafeteria. "Kiwi kept me up all night, and I guess I slept through my alarm"

"You don't set up alarms"

"Well…" Ulrich was at a loss for words.

"Are you ready for finals next week?" Yumi asked as she sipped from her coffee. "I will be, next week" Ulrich responded. "So you haven't started studying at all, then" Yumi deduced. "I will, just give me time" Ulrich coldly replied.

"What are you waiting for? It's not like you have much else going on. This isn't like last year when you were able to use Lyoko as an excuse"

"Lyoko wasn't an excuse" Ulrich said under his breath. Yumi looked into Ulrich's eyes, but they weren't the same eyes she fell in love with. The eyes she remembered were determined, fierce, and adventurous. The eyes she was looking into now showed signs of defeat.

"What happened to you, Ulrich?" Yumi asked, pleading with Ulrich to open up, but he just turned away. "Please, I want to help you" Yumi continued.

"Lyoko gave me a purpose. It gave me something to fight for. And now that Lyoko is gone, I just don't know what to do with myself." Ulrich answered, trying to avoid eye contact with Yumi. "I just need something to motivate me".

"What you need is a kick up the ass. Find opportunities; don't wait for them to come to you, because they never will".

"Lyoko came to me" Ulrich pouted. "Yes, but Jeremy gave you the chance to walk away, and you decided not to. You found the opportunity to go to Lyoko and took it" Yumi ended the conversation as she stood up from the table. "Wait…" Ulrich pleaded. "When you're ready to grow up, let me know" Yumi said as she walked away, leaving her coffee at the table.

Ulrich slumped onto the table and stared at the cup of coffee for several seconds, before reaching out to drink it. It would be pointless to let a half-empty cup of coffee go to waste.

* * *

If he wanted to, Odd could be an Olympic runner. The way he jumped out of his desk and to the classroom door once class was dismissed was a sight to behold. "A new world record!" Odd shouted as he exited the classroom, pumping his fists up in the air, unaware of his immediate surroundings.

"Congratulations" Odd heard from behind him, and he turned around to see Janice standing next to the door way. Janice was Odd's current romantic flame. "Oh, hey Janice, what's going on?" Odd said with his cheesy grin.

"You need to stop leaving me voicemails, Odd"

"Why, can't your inbox handle me?"

"Yes, but my phone bill cannot"

"Oh" Odd resigned, dropping his enthusiastic demeanor. "Sorry about that".

"Odd, what happened to you?" Janice asked. "Last year you barely cared about me. Every week it was some other girl, but now…" she dropped off at the end, trying to speak her mind politely. "I'm trying to be in a committed relationship" Odd said. Wrong choice of words.

"Ok, were not in a relationship. Never have been, never will be. You're too clingy"

"I'm just trying to improve myself. I don't need to be a womanizer"

"Well, while your womanizing was bad, your attachment is worse. You're like bad adhesive"

"Look, Janice, I'm sorry for trying to fill a hole in my life"

"Well, evidently that hole wasn't there last year. I suggest you stop trying to plug that hole up with attachment and find the stopgap that worked well before, because I can't take this anymore. You are suffocating me" she said, walking away from a now dejected Odd.

* * *

"Hey Yumi, wait up!" Yumi heard from behind her. She ignored the voice, and continued walking down the populated courtyard of Kadic Academy.

"Yumi, wait up" the voice said again, and Yumi turned around to see William rushing to catch up to her. "What do you want, William?" she snarled.

"I've barely seen you all semester. How are you?"

"I was doing great until I heard your weasel voice"

"Ah, still haven't forgiven me for the whole Scyphozoa thing?"

"Oh, I forgave you for that. However, you were dumb enough to let yourself get possessed again"

"Ok, so it's fool you once, shame on XANA, fool you twice, shame on me then".

Yumi abruptly stopped walking and turned to face William. "It doesn't have to do with XANA, or Lyoko, or anything other than your personality". "What about my personality?" William said with a smirk. Yumi slightly squinted and tilted her head. "You're arrogant"

"You might be confusing arrogance with confidence"

"That's a very arrogant thing to say"

"Look, Yumi" William said coldly. "I get that you don't want to give me another chance, but you and your friends don't have to treat me like I'm diseased"

"Ok, give me three reasons why we should show you respect"

"Easy. Firstly, I've saved your asses on numerous occasions, even if you time-wiped them out of existence. Second, I genuinely care for you, and third… well, I can't think of a third reason right now, but your grudge is still unjustified"

Yumi nodded. "Like I said, arrogant". She turned around and walked away, leaving William stunned.

* * *

Jeremy sat at his desk, tying furiously on his computer, constructing code for a virus. In the months since the supercomputer was shut down, Jeremy had kept himself busy by trying to recreate the XANA virus, but without all those annoying destructive tendencies.

When Franz Hopper set out on Project Carthage back in the 1970s, he had no idea what he was getting into. Working for the government means that your work will never remain yours. So he tried to destroy it with the XANA virus. Conceptually, the XANA virus was sound. A simple way to destroy invasive government projects. But it grew out of control and became a massive threat to the world. What if XANA could be recreated though, as it was originally intended to be? Without the pressure of the government? Imagine what Hopper could have created if he was able to operate outside of the government.

Jeremy continued typing away source code, despite the developing carpal tunnel. He had to keep working, to defend himself and his friends against whatever threat might pop up in the future.

int netlog(const char *pszFormat, ...)

{

char szHeadBuf[100];

int iHeadLen = 0;

va_list argList;

va_start(argList, pszFormat);

vsnprintf(szLineBuf+100, sizeof(szLineBuf)-110, pszFormat, argList);

szLineBuf[sizeof(szLineBuf)-10] = '\0';

An e-mail notification popped up in the corner of his screen. Jeremy clicked on the box, which pulled up his e-mail client. Jeremy ran the e-mail through two separate virus scanners, both of which came back clean, before opening the e-mail addressed from " .fr". So an e-mail from a French intelligence agency? Jeremy, bemused, opened the e-mail, which had no subject title and only contained three words in the body, all in caps:

"ALL ROADS END".

"…what… the hell…" Jeremy said to himself as he read the line of text. And that's when his computer caught fire.

* * *

_Special Agent _Sencaaff was not a pleasant woman to be around. Born in Germany and raised in Austria, she quickly rose through the ranks of the Direction Centrale du Renseignement Intérieur, France's homeland intelligence industry, thanks to her unrelenting determination to finish her mission at any cost. Despite being in her early 50s, she was an expert on hacking and cyber-warfare. Sencaaff operated out of the DCRI's main offices, a few miles north of Paris.

She was given her current post around two years ago, in the winter of '03, when sizeable and unexplainable electric discharges were being noticed Sceaux, France, less than an hour southwest of Paris. The unknown source of the discharges was labeled Designation 6 until it could be identified, although it never was. DCRI discovered the discharges when the local electrical plants were struggling to support the unknown designation. Whatever Designation 6 was, it was able to hide itself. Agents were sent into the field to figure out what was happening, but they kept turning up empty handed.

For years, she played a cat and mouse game, except she didn't know who the mouse was, and then, half a year ago, it all stopped. The electrical signature they could never get ahold of ceased. And then, two months ago, a name popped up.

"His name is Jeremy Belpois" Sencaaff was told by her superior, Agent Kopsa. "He's just a kid, why are we looking at him?" Sencaaff asked curiously.

"Whatever happened in Sceaux over the past 2 years, we have reason to believe he's in on it" Kopsa reported, handing Sencaaff a small folder. "We were never able to track the energy signature on Designation 6" Sencaaff noted as she flipped through the files. "No, but we were able to connect the electrical surge with spikes in Belopis' internet usage.

"I don't understand" Sencaaff lied, buying more time to read the classified documents. "We were able to trace small but noticeable spikes in Belopis' internet signature that happened whenever Designation 6 showed an electrical burst" Kopsa said, as he snatched the folder away from Sencaaff.

"We need you to find out how he is connected to Designation 6"

"That report says that he goes to the Kadic Academy"

"Is that an issue?"

Sencaaff took a deep breath. "No, just interesting. About a decade ago we found a refugee living around their campus, he taught there for a while. Probably a coincidence"

"I don't believe in coincidences" Kopsa retorted, as he walked out of the conference room.

Sencaaff didn't believe in coincidences either. The fact that she had ended up on this case was not a coincidence. She was exactly where she wanted to be.

Sencaaff pulled out her phone, opened her files, and pulled up a document labeled "1994". She scrolled through the document one last time, before deleting the document off her phone. "Let's begin" she said to herself with a smile.

* * *

**Author's Note:**

**Well, that's episode 1! Please let me know if you enjoyed the start and want to see it continue. Like with my previous stories I will aim to provide a 13 episode first season and we will take it from there.**

**Also, just for reference, the timeline of events I am using for this story are based off this, which is the most accurate recorded timeline I could find for CL: watch?v=I_UorU8KE40**


End file.
